jbkc - Jailbreaking does not effect itunes or app store & you update the OS the same way, however updating the OS could lose your jailbreak.. So before updating be sure to check the jailbreak is out for that OS.

If you decide to jailbreak there is an app on the regular app market called lookout security also doubles as a lowjack you sign up on the website and you can track your phone also make it scream if you lost it in ur house, but it is also a virus scanner and will scan non market apps for safety